Genotyping: raw RNA vs
RNA
- compare SNPs from 40 RNA BAM files to each other
- percentage values indicate the percentage of SNPs matched based on
gtcheck
- here, unfiltered/raw VCFs were used

Genotyping: filtered
RNA vs RNA
- here, use QC-filtered VCFs

Genotyping: DNA vs
RNA
- compare SNPs from 40 RNA BAM files to SNPs from donor Neurochip
data
- percentage values indicate the percentage of SNPs matched based on
gtcheck

- same as above, reorder DNA donor samples on x-axis

SessionInfo
## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.2.0 (2022-04-22)
## os macOS Big Sur/Monterey 10.16
## system x86_64, darwin17.0
## ui X11
## language (EN)
## collate en_GB.UTF-8
## ctype en_GB.UTF-8
## tz Europe/London
## date 2022-12-09
## pandoc 2.18 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/tools/ (via rmarkdown)
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date (UTC) lib source
## abind 1.4-5 2016-07-21 [1] CRAN (R 4.2.0)
## assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.0)
## backports 1.4.1 2021-12-13 [1] CRAN (R 4.2.0)
## broom 1.0.1 2022-08-29 [1] CRAN (R 4.2.0)
## bslib 0.4.1 2022-11-02 [1] CRAN (R 4.2.0)
## cachem 1.0.6 2021-08-19 [1] CRAN (R 4.2.0)
## callr 3.7.3 2022-11-02 [1] CRAN (R 4.2.0)
## car 3.1-1 2022-10-19 [1] CRAN (R 4.2.0)
## carData 3.0-5 2022-01-06 [1] CRAN (R 4.2.0)
## cli 3.4.1 2022-09-23 [1] CRAN (R 4.2.0)
## codetools 0.2-18 2020-11-04 [1] CRAN (R 4.2.0)
## colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.2.0)
## crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.0)
## crosstalk 1.2.0 2021-11-04 [1] CRAN (R 4.2.0)
## data.table * 1.14.6 2022-11-16 [1] CRAN (R 4.2.0)
## DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.0)
## devtools 2.4.5 2022-10-11 [1] CRAN (R 4.2.0)
## digest 0.6.30 2022-10-18 [1] CRAN (R 4.2.0)
## dplyr 1.0.10 2022-09-01 [1] CRAN (R 4.2.0)
## DT * 0.26 2022-10-19 [1] CRAN (R 4.2.0)
## ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0)
## evaluate 0.18 2022-11-07 [1] CRAN (R 4.2.0)
## fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.0)
## farver 2.1.1 2022-07-06 [1] CRAN (R 4.2.0)
## fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0)
## fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.0)
## generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0)
## ggplot2 * 3.4.0 2022-11-04 [1] CRAN (R 4.2.0)
## ggpubr * 0.5.0 2022-11-16 [1] CRAN (R 4.2.0)
## ggsignif 0.6.4 2022-10-13 [1] CRAN (R 4.2.0)
## glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0)
## gtable 0.3.1 2022-09-01 [1] CRAN (R 4.2.0)
## highr 0.9 2021-04-16 [1] CRAN (R 4.2.0)
## htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.0)
## htmlwidgets 1.5.4 2021-09-08 [1] CRAN (R 4.2.0)
## httpuv 1.6.6 2022-09-08 [1] CRAN (R 4.2.0)
## jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.2.0)
## jsonlite 1.8.3 2022-10-21 [1] CRAN (R 4.2.0)
## knitr * 1.41 2022-11-18 [1] CRAN (R 4.2.0)
## labeling 0.4.2 2020-10-20 [1] CRAN (R 4.2.0)
## later 1.3.0 2021-08-18 [1] CRAN (R 4.2.0)
## lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.0)
## magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
## memoise 2.0.1 2021-11-26 [1] CRAN (R 4.2.0)
## mime 0.12 2021-09-28 [1] CRAN (R 4.2.0)
## miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.2.0)
## munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0)
## pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.0)
## pkgbuild 1.4.0 2022-11-27 [1] CRAN (R 4.2.0)
## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
## pkgload 1.3.2 2022-11-16 [1] CRAN (R 4.2.0)
## prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.0)
## processx 3.8.0 2022-10-26 [1] CRAN (R 4.2.0)
## profvis 0.3.7 2020-11-02 [1] CRAN (R 4.2.0)
## promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.2.0)
## ps 1.7.2 2022-10-26 [1] CRAN (R 4.2.0)
## purrr 0.3.5 2022-10-06 [1] CRAN (R 4.2.0)
## R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0)
## Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.2.0)
## remotes 2.4.2 2021-11-30 [1] CRAN (R 4.2.0)
## rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.0)
## rmarkdown 2.18 2022-11-09 [1] CRAN (R 4.2.0)
## rstatix 0.7.1 2022-11-09 [1] CRAN (R 4.2.0)
## rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.0)
## sass 0.4.4 2022-11-24 [1] CRAN (R 4.2.0)
## scales 1.2.1 2022-08-20 [1] CRAN (R 4.2.0)
## sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0)
## shiny 1.7.3 2022-10-25 [1] CRAN (R 4.2.0)
## stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.0)
## stringr 1.5.0 2022-12-02 [1] CRAN (R 4.2.0)
## tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.0)
## tidyr 1.2.1 2022-09-08 [1] CRAN (R 4.2.0)
## tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.0)
## urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.2.0)
## usethis 2.1.6 2022-05-25 [1] CRAN (R 4.2.0)
## utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0)
## vctrs 0.5.1 2022-11-16 [1] CRAN (R 4.2.0)
## withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0)
## xfun 0.35 2022-11-16 [1] CRAN (R 4.2.0)
## xtable 1.8-4 2019-04-21 [1] CRAN (R 4.2.0)
## yaml 2.3.6 2022-10-18 [1] CRAN (R 4.2.0)
##
## [1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
##
## ──────────────────────────────────────────────────────────────────────────────